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- PDB-5em4: Structure of CYP2B4 F244W in a ligand free conformation -

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Basic information

Entry
Database: PDB / ID: 5em4
TitleStructure of CYP2B4 F244W in a ligand free conformation
ComponentsCytochrome P450 2B4
KeywordsOXIDOREDUCTASE / Cytochrome P450 / monooxygenase
Function / homology
Function and homology information


arachidonate epoxygenase activity / epoxygenase P450 pathway / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / xenobiotic metabolic process / iron ion binding / heme binding / endoplasmic reticulum membrane
Similarity search - Function
Cytochrome P450, E-class, group I, CYP2B-like / : / Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 ...Cytochrome P450, E-class, group I, CYP2B-like / : / Cytochrome P450, E-class, group I / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 2B4
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsShah, M.B. / Stout, C.D. / Halpert, J.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES003619 United States
CitationJournal: Biochemistry / Year: 2016
Title: Coumarin Derivatives as Substrate Probes of Mammalian Cytochromes P450 2B4 and 2B6: Assessing the Importance of 7-Alkoxy Chain Length, Halogen Substitution, and Non-Active Site Mutations.
Authors: Liu, J. / Shah, M.B. / Zhang, Q. / Stout, C.D. / Halpert, J.R. / Wilderman, P.R.
History
DepositionNov 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 2B4
B: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1108
Polymers111,8992
Non-polymers3,2116
Water25214
1
A: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5554
Polymers55,9491
Non-polymers1,6063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome P450 2B4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5554
Polymers55,9491
Non-polymers1,6063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.030, 92.030, 151.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A28 - 135
2111B28 - 135
1211A140 - 492
2211B140 - 492

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.499359, -0.866395, -0.000461), (-0.866395, 0.499359, -6.5E-5), (0.000287, 0.000367, -1)0.04986, 53.16342, 50.84598

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Components

#1: Protein Cytochrome P450 2B4 / CYPIIB4 / Cytochrome P450 isozyme 2 / Cytochrome P450 LM2 / Cytochrome P450 type B0 / Cytochrome P450 type B1


Mass: 55949.355 Da / Num. of mol.: 2 / Mutation: H226Y, F244W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CYP2B4 / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3 / References: UniProt: P00178, unspecific monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CM5 / 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE / 5-CYCLOHEXYLPENTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE / CYMAL-5


Mass: 494.573 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H42O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES pH 7.0 and 10% w/v polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.02→44.08 Å / Num. obs: 24530 / % possible obs: 96.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.56 / Net I/σ(I): 2.5
Reflection shellResolution: 3.02→3.09 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.1 / % possible all: 93.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MVR

3mvr


Resolution: 3.02→44.08 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.861 / SU B: 24.075 / SU ML: 0.42 / Cross valid method: THROUGHOUT / ESU R Free: 0.501 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1297 5 %RANDOM
Rwork0.228 ---
obs0.231 24530 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 3.02→44.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7130 0 222 14 7366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197644
X-RAY DIFFRACTIONr_bond_other_d0.0020.027169
X-RAY DIFFRACTIONr_angle_refined_deg1.6472.00210409
X-RAY DIFFRACTIONr_angle_other_deg1.035316456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.345914
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92822.865342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.057151160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.191559
X-RAY DIFFRACTIONr_chiral_restr0.1730.21174
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218489
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021838
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 6990 / Type: tight thermal / Rms dev position: 4.04 Å / Weight position: 0.5
LS refinement shellResolution: 3.02→3.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 86 -
Rwork0.292 1650 -
obs--85.18 %

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